The film opens during the American Civil War. In a United States Army field hospital, First Lieutenant John J. Dunbar (Kevin Costner) learns that his injured leg is to be amputated. Seeing the plight of fellow soldiers with amputated legs, Dunbar leaves the hospital, steals a cavalry horse, and attempts suicide by riding across the no man’s land between the opposing Union and Confederate positions. His action unexpectedly rallies the Union soldiers, who storm the distracted Confederate defenses to win the battle. Impressed by Dunbar’s actions, the commanding general of the Union forces, Lieutenant General Tide (Donald Hotton), summons his personal surgeon to save Dunbar’s leg. Tide declares Dunbar to be a hero and awards him Cisco, the horse who carried him in battle as well as offering Dunbar his choice of posting. Dunbar requests a transfer to the western frontier and soon after his leg heals he arrives at a fort which is a gateway to the west. This is where he begins to record his frontier experiences in a journal read in voice over.

Dunbar meets Major Fambrough (Maury Chaykin). The Major has slipped into alcohol-fueled delusions of grandeur (apparently believing he is a king and Dunbar a medieval knight). Fambrough scribbles out Dunbar’s orders to report to Captain Cargill at Fort Sedgwick and pairs him off with an uncouth drayage teamster named Timmons (Robert Pastorelli), who is to convey him to his post. After they depart, Fambrough shoots himself in the head.

…

As Dances With Wolves and Stands With A Fist leave the camp, Wind In His Hair cries out that Dances With Wolves will always be his friend. Soon after, a column of US Cavalry and Pawnee army scouts arrive to find the former Sioux camp site empty. Before the end credits, a note explains that a few years later the last remnants of free Sioux were subjugated to the U.S. Government, ending the conquest of the Western frontier states.

On July 2, a giant alien mothership enters orbit around Earth and deploys several dozen saucer-shaped “destroyer” spacecraft, each 15 miles (24 km) in width. As the destroyers take positions over some of Earth’s major cities, David Levinson (Jeff Goldblum), an MIT graduate working for a cable company in New York City, discovers hidden satellite transmissions which he believes to be a timer counting down to a coordinated attack by the aliens. With the help of his ex-wife Constance Spano (Margaret Colin), a White House employee, he and his father Julius (Judd Hirsch) gain entrance into the Oval Office to warn President Thomas J. Whitmore (Bill Pullman) of the impending attack. The President immediately orders large-scale evacuations of the targeted cities, but the aliens attack with advanced directed-energy weapons before these could occur. The President, portions of his staff, and the Levinsons narrowly escape aboard Air Force One as the destroyers simultaneously lay waste to Washington, D.C, New York City, Los Angeles, and several other major cities around the world.

On July 3, the United States conducts a coordinated counterattack; the movie follows the Black Knights, a squadron of Marine Corps F/A-18 Hornets, as they participate in an assault on a destroyer near the destroyed city of Los Angeles. Their weapons fail to penetrate the craft’s force field, and it responds by releasing scores of smaller “attacker” ships which are similarly shielded and armed with directed-energy weapons, and a one-sided dogfight ensues. Captain Steven Hiller (Will Smith) survives the attack by luring a single attacker to the Grand Canyon.[4] There, he blinds the alien with the braking parachute on his jet and ejects just before running out of fuel, causing both to crash in the desert. Having parachuted to safety, he subdues the injured alien. Hiller is picked up by Russell Casse (Randy Quaid), who is traveling across the desert with a group of refugees in a convoy of RVs. They take the captured alien to nearby Area 51, commanded by Major Mitchell (Adam Baldwin), where the President and his remaining staff have also landed. Here, it is shown that Area 51 conceals a top secret facility housing a repaired attacker and three alien bodies recovered from Roswell in 1947.

…

With the successful implantation of the virus, President Whitmore leads the American jet fighters against an alien destroyer on approach to Area 51. Although the aliens now lack shields, the fighters’ supply of missiles are quickly exhausted against the colossal craft and its large complement of assault ships. The underside of the alien craft opens up as its directed-energy weapon prepares to fire on the base. Russell possesses the last remaining missile, but his firing mechanism jams; changing his plan, he pilots his aircraft into the alien weapon in a kamikaze attack. The ensuing explosion causes a chain reaction which annihilates the ship. Using this same method, human resistance forces around the world destroy the remainder of the alien ships and saving several surviving major cities, while the nuclear device planted by Hiller and Levinson destroys the alien mothership soon after the duo escape. Hiller and Levinson return unharmed, crash-landing their captured alien fighter in the desert close to Area 51. The world celebrates, and the film ends as the main characters watch debris from the mothership enter the atmosphere like fireworks.

Donnie Darko (played by Jake Gyllenhaal) is a troubled teenager in suburban Virginia in October 1988. He appears to be suffering the symptoms of paranoid schizophrenia. At the start of the film, he has recently stopped taking his medication. His parents, Rose and Eddie (Mary McDonnell and Holmes Osborne) and his sisters, Elizabeth and Samantha (Maggie Gyllenhaal and Daveigh Chase), are concerned about him. One night at dinner, Donnie and his sister get into a profane argument during which Elizabeth reveals she knows Donnie is no longer taking his medication. Rose confronts Donnie in his bedroom asking him where her little boy has gone and who the stranger is who has taken his place. As she leaves the room, she hears him call her a “bitch” from the other side of the door. Feeling guilty, Donnie resumes taking his medication. On October 2, however, he sleepwalks and meets Frank (James Duval), a man in a menacing bunny costume. Frank tells him that in 28 days, 6 hours, 42 minutes and 12 seconds, the world will end. While he is outside, a jet engine mysteriously crashes through the roof of the Darkos’ house, destroying Donnie’s bedroom.

As Eddie drives Donnie to the office of Dr. Thurman (Katharine Ross), Donnie’s therapist, Eddie nearly runs over Roberta Sparrow, also known as “Grandma Death” (Patience Cleveland). A senile old woman who spends her days walking back and forth from her house to the mailbox across the street, Grandma Death whispers in Donnie’s ear that all living things die alone. This greatly troubles Donnie, who worries that life has no meaning.

…

It is once again October 2. Donnie is in bed, creating a predestination paradox. On this occasion, he chooses to stay in bed, presumably to prevent the harm he caused to several lives in the tangent universe, including Gretchen, the girlfriend he will never meet. Shortly after he goes to sleep, the jet engine from the red eye flight on October 30 crashes through the roof, killing him. In a deleted scene from the director’s cut DVD it is revealed that he was actually impaled by a piece of wood from the broken roof while performing an act of self-gratification, though the removal of this from this film proper makes its canonicity questionable. All the people affected by Donnie’s actions awake as if from a nightmare, having some fragments of memories remaining: Frank, Elizabeth’s boyfriend, subconsciously touches his right eye. Jim Cunningham, perhaps in guilt and remorse for being a pedophile, a hypocrite and phony, awakens crying. As Donnie’s body is taken away, Gretchen, having never met Donnie, rides by the Darkos’ house on her bicycle. She learns from a neighbor boy what has happened and waves to Rose, who is smoking a cigarette. There is an air of mutual recognition between them.